VPS53 [The Human Chemical-Genetic Interaction Map Project]

This page is read only. You can view the source, but not change it. Ask your administrator if you think this is wrong.
======= VPS53 =======


== Gene Information ==
  * **<color #00a2e8>Official Symbol</color>**: VPS53
  * **<color #00a2e8>Official Name</color>**: VPS53 subunit of GARP complex
  * **<color #00a2e8>Aliases and Previous Symbols</color>**: N/A
  * **<color #00a2e8>Entrez ID</color>**: [[https://www.ncbi.nlm.nih.gov/gene/?term=55275|55275]]
  * **<color #00a2e8>UniProt</color>**: [[https://www.uniprot.org/uniprot/Q5VIR6|Q5VIR6]]
  * **<color #00a2e8>Interactions</color>**: [[https://thebiogrid.org/search.php?search=VPS53&organism=9606|BioGRID]]
  * **<color #00a2e8>PubMed articles</color>**: [[https://www.ncbi.nlm.nih.gov/pubmed/?term=gene%20VPS53|Open PubMed]]
  * **<color #00a2e8>OMIM</color>**: [[https://omim.org/entry/615850|Open OMIM]]

== Function Summary ==
  * **<color #00a2e8>Entrez Summary</color>**:  This gene encodes a protein with sequence similarity to the yeast Vps53p protein. Vps53p is involved in retrograde vesicle trafficking in late Golgi. [provided by RefSeq, Jul 2008]. 
  * **<color #00a2e8>UniProt Summary</color>**:  Acts as component of the GARP complex that is involved in retrograde transport from early and late endosomes to the trans-Golgi network (TGN). The GARP complex is required for the maintenance of the cycling of mannose 6-phosphate receptors between the TGN and endosomes, this cycling is necessary for proper lysosomal sorting of acid hydrolases such as CTSD (PubMed:15878329, PubMed:18367545). Acts as component of the EARP complex that is involved in endocytic recycling. The EARP complex associates with Rab4-positive endosomes and promotes recycling of internalized transferrin receptor (TFRC) to the plasma membrane (PubMed:25799061). {ECO:0000269|PubMed:15878329, ECO:0000269|PubMed:18367545, ECO:0000269|PubMed:25799061}.

<button type='primary' size='sm' modal='Pfam_Domains'>Pfam Domains</button>
<button type='primary' size='sm' modal='GO_terms'>GO Terms</button>


<modal id='Pfam_Domains' size='lg' title='Pfam Domains'>
|DUF2450|
|Vps53 N|
</modal>

<modal id='GO_terms' size='lg' title='GO Terms'>
|GARP complex|
|EARP complex|
|endocytic recycling|
|trans-Golgi network membrane|
|retrograde transport, endosome to Golgi|
|lysosomal transport|
|recycling endosome|
|vacuolar transport|
|cytosolic transport|
|endosome membrane|
|endosomal transport|
|perinuclear region of cytoplasm|
|Golgi apparatus|
|protein transport|
|intracellular transport|
|peptide transport|
|amide transport|
|establishment of protein localization|
|establishment of localization in cell|
|nitrogen compound transport|
|vesicle-mediated transport|
|membrane|
</modal>
\\

 === CRISPR Data ===
<button type='primary' size='small' modal='Compound_Hit'>Compound Hit</button>
<button type='primary' size='small' modal='Most_Correlated_Genes'>Most Correlated Genes in Chemogenomics</button>
<button type='primary' size='small' modal='Essential_Avana'>Tissues where Essential in the Avana Dataset (DepMap 20Q1)</button>

<modal id='Compound_Hit' size='lg' title='Compound Hit'>
^Screen^Score^
|[[:results:exp25|Oligomycin-A 2μM R00 exp25]]|-2.26|
|[[:results:exp376|Losmapimod 1μM R07 exp376]]|-2.2|
|[[:results:exp7|Bortezomib 0.05μM R00 exp7]]|-2.18|
|[[:results:exp468|CB-5083 0.4μM R08 exp468]]|-2.06|
|[[:results:exp48|Mubritinib 0.2μM R01 exp48]]|-2.02|
|[[:results:exp529|Thimerosal 0.85μM R08 exp529]]|-2.02|
|[[:results:exp443|SNS-032 15μM R08 exp443]]|-2|
|[[:results:exp126|GSK461364A 0.1μM R03 exp126]]|-1.98|
|[[:results:exp306|Rapamycin 2μM R07 exp306]]|-1.95|
|[[:results:exp401|SNS-032 25μM R07 exp401]]|-1.93|
|[[:results:exp96|BI-2536 0.02μM R03 exp96]]|-1.92|
|[[:results:exp59|UMK57 1μM R01 exp59]]|-1.87|
|[[:results:exp382|Palbociclib 1μM R07 exp382]]|-1.86|
|[[:results:exp211|AICAR 240μM R05 exp211]]|-1.85|
|[[:results:exp262|Alda-1 10μM R06 exp262]]|-1.84|
|[[:results:exp290|LLY-283 2.6μM R06 exp290]]|-1.81|
|[[:results:exp45|Docetaxel 0.002μM R01 exp45]]|-1.78|
|[[:results:exp22|MLN-4924 2μM R00 exp22]]|-1.78|
|[[:results:exp95|BI-2536 0.0042μM R03 exp95]]|-1.75|
|[[:results:exp80|RO-3307 4.7μM R02 exp80]]|-1.74|
|[[:results:exp434|Vemurafenib 6.6μM R08 exp434]]|-1.74|
|[[:results:exp61|YM155 0.0002μM R01 exp61]]|-1.72|
|[[:results:exp459|Bleomycin 5μM R08 exp459]]|-1.7|
|[[:results:exp93|DABN racemic mixture R03 exp93]]|-1.7|
|[[:results:exp162|BI-D1870 2μM R04 exp162]]|1.88|
</modal>

<modal id='Most_Correlated_Genes' size='lg' title='Most Correlated Genes in Chemogenomics'>
^Gene^Correlation^
|[[:human genes:v:vps28|VPS28]]|0.46|
|[[:human genes:r:rrp9|RRP9]]|0.406|
|[[:human genes:t:trappc11|TRAPPC11]]|0.404|
</modal>

<modal id='Essential_Avana' size='lg' title='Tissues where Essential in the Avana Dataset (DepMap 20Q1)'>
Global Fraction of Cell Lines Where Essential: 0/739
^Tissue^Fraction Of Cell Lines Where Essential^
|1290807.0|0/1|
|909776.0|0/1|
|bile duct|0/28|
|blood|0/28|
|bone|0/26|
|breast|0/33|
|central nervous system|0/56|
|cervix|0/4|
|colorectal|0/17|
|esophagus|0/13|
|fibroblast|0/1|
|gastric|0/16|
|kidney|0/21|
|liver|0/20|
|lung|0/75|
|lymphocyte|0/16|
|ovary|0/26|
|pancreas|0/24|
|peripheral nervous system|0/16|
|plasma cell|0/15|
|prostate|0/1|
|skin|0/24|
|soft tissue|0/9|
|thyroid|0/2|
|upper aerodigestive|0/22|
|urinary tract|0/29|
|uterus|0/5|
</modal>

== Essentiality in NALM6  ==
    * **<color #00a2e8>Essentiality Rank</color>**: 1015
    * **<color #00a2e8>Expression level (log2 read counts)</color>**: 6.39 
<button type='primary' size='small' modal='Dist_expr'>Expression Distribution</button>
<modal id='Dist_expr' size='lg' title='VPS53 Expression in NALM6 Cells: 6.39'>
{{:chemogenomics:nalm6 dist.png?nolink |}}
</modal>